Microbial associations for pneumonia causative agents and level of their resistance to antimicrobial drugs during a new coronavirus infection pandemic

Abstract

Introduction. Bacterial coinfection and secondary bacterial infection are considered critical risk factors for the severity and mortality of SARS-CoV-2-caused pneumonia. The aim of the study was to analyze a pattern of microbial associations between K. pneumoniae and A. baumannii isolated from the lower respiratory tract discharge and sectional material (lung tissue) of patients diagnosed with pneumonia, and to compare resistance level in monoculture and associations during new coronavirus infection pandemic. Materials and methods. A bacteriological study of 2689 sputum and bronchial washing samples from patients at infectious diseases hospitals, and 1411 lung pathological material samples was carried out. Bacterial isolates were identified by mass spectrometry. Antibiotic sensitivity for isolates was determined by the disk diffusion method. Genetic determinants of resistance to beta-lactam antibiotics were detected by PCR. Statistical data processing was performed using SPSS version 22 software. Results. K. pneumoniae and A. baumannii isolates were predominantly found in two- and three-pathogen associations. It was established that the resistance level of K. pneumoniae isolates in association with A. baumannii is significantly higher compared to that in monoculture for all antimicrobial drugs studied. At the same time, K. pneumoniae in combination with Candida spp. vs monoculture showed significantly lower level of resistance to ciprofloxacin, amikacin, cefotaxime, ceftazidime and amoxicillin/clavulanic acid. K. pneumoniae isolates carried resistance determinants to extended-spectrum beta-lactamases: OXA-48 — (22.5%), OXA-51 — (5.6%), OXA-23 — (4.2%), KPC — 70.9%, NDM — 7%. Of these, 14.1% of strains had the ability to co-produce serine carbapenemases OXA-48 and KPC. Sputum and lung tissue A. baumannii isolates exhibited extremely high multiple resistance regardless of their associations with other microorganisms. Microbiome species similarity in the lower respiratory tract and lung tissue discharge was revealed. The proportion of lung tissue vs sputum resistant strains of K. pneumoniae and A. baumannii was significantly higher. Conclusion. The detection of of multiple drug resistant K. pneumoniae and A. baumannii isolates as well as their associations may indicate aggravated pneumonia severity.